[med-svn] [Git][med-team/nipy][master] 2 commits: initialize changelog.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sat Feb 4 14:09:59 GMT 2023
Étienne Mollier pushed to branch master at Debian Med / nipy
Commits:
01de33f4 by Étienne Mollier at 2023-02-04T15:07:28+01:00
initialize changelog.
- - - - -
12a4fbea by Étienne Mollier at 2023-02-04T15:07:44+01:00
nibabel5.0.0.patch: update following review upstream
Thanks: Chris Markiewicz and Yaroslav Halchenko
- - - - -
2 changed files:
- debian/changelog
- debian/patches/nibabel5.0.0.patch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+nipy (0.5.0-8) UNRELEASED; urgency=medium
+
+ [ Yaroslav Halchenko ]
+ * removed myself and Michael since we have not attended to this package for
+ awhile
+
+ -- Étienne Mollier <emollier at debian.org> Sat, 04 Feb 2023 15:07:02 +0100
+
nipy (0.5.0-7) unstable; urgency=medium
* Team upload.
=====================================
debian/patches/nibabel5.0.0.patch
=====================================
@@ -1,9 +1,11 @@
Description: port py3k calls to nibabel 5.0.0
The nibabel.py3k module doesn't exist anymore. numpy.compat.py3k is fetched
- directly instead.
+ directly instead. A number of Nifti1Image class instantiations also need
+ adjustment, since masks of int64 or uint64 are not tolerated implicitly
+ anymore.
Author: Étienne Mollier <emollier at debian.org>
Bug-Debian: https://bugs.debian.org/1030138
-Forwarded: no
+Forwarded: https://github.com/nipy/nipy/pull/498
Last-Update: 2023-01-31
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
@@ -68,7 +70,7 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
assert_false(is_xyz_affable(img4_r))
assert_raises(AxesError, xyz_affine, img4_r)
- nimg = nib.Nifti1Image(arr, aff)
-+ nimg = nib.Nifti1Image(arr, aff, dtype=arr.dtype)
++ nimg = nib.Nifti1Image(arr.astype('float'), aff)
assert_true(is_xyz_affable(nimg))
assert_array_equal(xyz_affine(nimg), aff)
# Any dimensions not spatial, AxesError
@@ -77,109 +79,80 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
assert_equal(img.coordmap, img_t0_r.coordmap)
# Test against nibabel image
- nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
-+ nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]), dtype=arr.dtype)
++ nimg = nib.Nifti1Image(arr.astype('float'), np.diag([2,3,4,1]))
nimg_r = as_xyz_image(nimg)
assert_true(nimg is nimg_r)
# It's sometimes impossible to make an xyz affable image
--- nipy.orig/nipy/labs/spatial_models/tests/test_discrete_domain.py
+++ nipy/nipy/labs/spatial_models/tests/test_discrete_domain.py
-@@ -130,7 +130,7 @@
- toto = np.ones(shape[:3])
- affine = np.random.randn(4, 4)
- affine[3:, 0:3] = 0
-- nim = Nifti1Image(toto, affine)
-+ nim = Nifti1Image(toto, affine, dtype=toto.dtype)
- ddom = domain_from_image(nim)
- ref = np.sum(toto) * np.absolute(np.linalg.det(affine))
- assert_almost_equal(np.sum(ddom.local_volume), ref)
-@@ -142,8 +142,8 @@
+@@ -142,7 +142,7 @@
mask = np.random.randn(*shape[:3]) > .5
noise = np.random.randn(*shape[:3])
affine = np.eye(4)
- mim = Nifti1Image(mask.astype('u8'), affine)
-- nim = Nifti1Image(noise, affine)
-+ mim = Nifti1Image(mask.astype('u8'), affine, dtype=mask.astype('u8').dtype)
-+ nim = Nifti1Image(noise, affine, dtype=noise.dtype)
++ mim = Nifti1Image(mask.astype('u1'), affine)
+ nim = Nifti1Image(noise, affine)
ddom = grid_domain_from_image(mim)
ddom.make_feature_from_image(nim, 'noise')
- assert_almost_equal(ddom.features['noise'], noise[mask])
-@@ -163,7 +163,7 @@
- toto = np.ones(shape[:3])
- affine = np.random.randn(4, 4)
- affine[3:, 0:3] = 0
-- nim = Nifti1Image(toto, affine)
-+ nim = Nifti1Image(toto, affine, dtype=toto.dtype)
- ddom = grid_domain_from_image(nim)
- ref = np.sum(toto) * np.absolute(np.linalg.det(affine[:3, 0:3]))
- assert_almost_equal(np.sum(ddom.local_volume), ref)
--- nipy.orig/nipy/labs/spatial_models/tests/test_mroi.py
+++ nipy/nipy/labs/spatial_models/tests/test_mroi.py
-@@ -205,8 +205,10 @@
+@@ -205,8 +205,8 @@
# Test example runs correctly
eg_img = pjoin(dirname(__file__), 'some_blobs.nii')
nim = load(eg_img)
- mask_image = Nifti1Image((nim.get_data() ** 2 > 0).astype('u8'),
- get_affine(nim))
+ arr = nim.get_data() ** 2 > 0
-+ mask_image = Nifti1Image(arr.astype('u8'),
-+ get_affine(nim),
-+ dtype=arr.astype('u8').dtype)
++ mask_image = Nifti1Image(arr.astype('u1'), get_affine(nim))
domain = grid_domain_from_image(mask_image)
data = nim.get_data()
values = data[data != 0]
--- nipy.orig/nipy/labs/spatial_models/tests/test_parcel_io.py
+++ nipy/nipy/labs/spatial_models/tests/test_parcel_io.py
-@@ -17,7 +17,9 @@
+@@ -17,7 +17,7 @@
"""
n_parcels = 20
shape = (10, 10, 10)
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
-+ mask_image = Nifti1Image(np.ones(shape),
-+ np.eye(4),
-+ dtype=np.ones(shape).dtype)
++ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
wim = mask_parcellation(mask_image, n_parcels)
assert_equal(np.unique(wim.get_data()), np.arange(n_parcels))
-@@ -33,8 +35,10 @@
+@@ -33,8 +33,8 @@
with InTemporaryDirectory():
for subject in range(n_subjects):
path = 'mask%s.nii' % subject
- save(Nifti1Image((rng.rand(*shape) > .1).astype('u8'),
- np.eye(4)), path)
+ arr = rng.rand(*shape) > .1
-+ save(Nifti1Image(arr.astype('u8'), np.eye(4),
-+ dtype=arr.astype('u8').dtype),
-+ path)
++ save(Nifti1Image(arr.astype('u1'), np.eye(4)), path)
mask_images.append(path)
wim = mask_parcellation(mask_images, n_parcels)
-@@ -47,7 +51,8 @@
+@@ -47,7 +47,7 @@
# Generate an image
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
-+ mask_image = Nifti1Image(np.ones(shape), np.eye(4),
-+ dtype=np.ones(shape).dtype)
++ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
surrogate_3d_dataset(mask=mask_image, out_image_file='image.nii')
-@@ -67,7 +72,8 @@
+@@ -67,7 +67,7 @@
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
method = 'ward'
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
-+ mask_image = Nifti1Image(np.ones(shape), np.eye(4),
-+ dtype=np.ones(shape).dtype)
++ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
data_image = ['image_%d.nii' % i for i in range(5)]
-@@ -88,7 +94,8 @@
+@@ -88,7 +88,7 @@
shape = (10, 10, 10)
n_parcel, nn, mu = 10, 6, 1.
method = 'ward'
- mask_image = Nifti1Image(np.ones(shape), np.eye(4))
-+ mask_image = Nifti1Image(np.ones(shape), np.eye(4),
-+ dtype=np.ones(shape).dtype)
++ mask_image = Nifti1Image(np.ones(shape).astype('u1'), np.eye(4))
with InTemporaryDirectory() as dir_context:
surrogate_3d_dataset(n_subj=10, mask=mask_image,
out_image_file='image.nii')
@@ -190,47 +163,36 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
>>> import nibabel as nib
->>> nimg = nib.Nifti1Image(data, affine)
-+>>> nimg = nib.Nifti1Image(data, affine, dtype=data.dtype)
++>>> nimg = nib.Nifti1Image(data.astype('float'), affine)
>>> xyz_affine(nimg)
array([[ 2., 0., 0., 0.],
[ 0., 3., 0., 0.],
-@@ -132,7 +132,7 @@
- Nibabel images always have xyz affines
-
- >>> import nibabel as nib
-- >>> nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
-+ >>> nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]), dtype=arr.dtype)
- >>> xyz_affine(nimg)
- array([[ 2., 0., 0., 0.],
- [ 0., 3., 0., 0.],
@@ -195,7 +195,7 @@
Nibabel images always have xyz affines
>>> import nibabel as nib
- >>> nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]))
-+ >>> nimg = nib.Nifti1Image(arr, np.diag([2,3,4,1]), dtype=arr.dtype)
++ >>> nimg = nib.Nifti1Image(arr.astype('float'), np.diag([2,3,4,1]))
>>> is_xyz_affable(nimg)
True
"""
--- nipy.orig/nipy/labs/spatial_models/parcel_io.py
+++ nipy/nipy/labs/spatial_models/parcel_io.py
-@@ -54,7 +54,8 @@
+@@ -53,7 +53,7 @@
+ else:
# mask_images should be a list
mask_data = intersect_masks(mask_images, threshold=0) > 0
- mask = Nifti1Image(mask_data.astype('u8'),
-- get_affine(load(mask_images[0])))
-+ get_affine(load(mask_images[0])),
-+ dtype=mask_data.astype('u8').dtype)
+- mask = Nifti1Image(mask_data.astype('u8'),
++ mask = Nifti1Image(mask_data.astype('u1'),
+ get_affine(load(mask_images[0])))
domain = grid_domain_from_image(mask)
- cent, labels, J = kmeans(domain.coord, nb_parcel)
-@@ -100,7 +101,8 @@
+@@ -99,7 +99,7 @@
+ else:
# mask_images should be a list
grp_mask = intersect_masks(mask_images, threshold=ths) > 0
- mask = Nifti1Image(grp_mask.astype('u8'),
-- get_affine(load(mask_images[0])))
-+ get_affine(load(mask_images[0])),
-+ dtype=grp_mask.astype('u8').dtype)
+- mask = Nifti1Image(grp_mask.astype('u8'),
++ mask = Nifti1Image(grp_mask.astype('u1'),
+ get_affine(load(mask_images[0])))
# build the domain
- domain = grid_domain_from_image(mask, nn=6)
View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/8c92980857f25358762e57ccee200453ffaa85d6...12a4fbea8c99c1e5dc07ee81bc3da1a450617050
--
View it on GitLab: https://salsa.debian.org/med-team/nipy/-/compare/8c92980857f25358762e57ccee200453ffaa85d6...12a4fbea8c99c1e5dc07ee81bc3da1a450617050
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